Bycatch estimation data setup

Sets global conditions, makes a preliminary data summary and data checks (make plots and tables of the data).

Usage

bycatchSetup(
  obsdat,
  logdat,
  yearVar,
  obsEffort,
  logEffort,
  obsCatch,
  catchUnit,
  catchType,
  logNum,
  sampleUnit,
  factorVariables,
  numericVariables,
  EstimateBycatch = TRUE,
  baseDir = getwd(),
  runName,
  runDescription,
  common,
  sp,
  reportType = "html"
)

Arguments

obsdat

Observer data set

logdat

Logbook data set

yearVar

Character. The column name of the year variable in obsdat and logdat. Both input files must contain the same variable name for year.

obsEffort

Character. The column name of the effort variable in obsdat. This variable must have the same effort units as logEffort

logEffort

Character. The column name of the effort variable in logdat. Optional and only used when estimating bycatch. This variable must have the same effort units as obsEffort

obsCatch

Character vector. The name of the column(s) in obsdat that contain catch. If it is a vector, order of variable names must follow the same order as names provided in common and sp

catchUnit

Character vector. Give units of catch (e.g., number) to go in plot labels. Must be a vector of the same length as sp

catchType

Character vector. Give type of catch (e.g., dead discards) to go in plot labels. Must be a vector of the same length as sp

logNum

Character vector. The name of the column in logdat that gives the number of sample units (e.g., trips or sets). If the logbook data is not aggregated (i.e. each row is a sample unit) set value to NA

sampleUnit

Character. What is the sample unit in logdat? e.g. sets or trips.

factorVariables

Character vector. Specify which variables should be interpreted as categorical, ensuring factor format on these variables. These variables must have identical names and factor levels in obsdat and logdat

numericVariables

Character vector. Specify which variables should be interpreted as numeric. These variables must have identical names in obsdat and logdat. If there are no numeric variables, set numericVariables=NA.

EstimateBycatch

Logical. Defaults to TRUE. If TRUE, you must provide logbook data or some other source of total effort to logdat. FALSE will produced data summaries of obsdat only.

baseDir

Character. A directory to save output. Defaults to current working directory.

runName

Characer. Give a name to the run, which will be used to set up a directory for the outputs

runDescription

Character. Brief summary of the run, which will be used to set up a directory for the outputs

common

Character vector. Provide a common name for the species used in output filess. Can be a vector of names to do multiple species at the same time.

sp

Character vector. Provide a scientific name for the species used in output files. Can be a vector of names to do multiple species at the same time

reportType

Character. Choose type of report to be produced. Options are html (default), pdf or both.

Examples

if (FALSE) { # \dontrun{
library(BycatchEstimator)
setupObj<-bycatchSetup(
obsdat = obsdatExample,
logdat = logdatExample,
yearVar = "Year",
obsEffort = "sampled.sets",
logEffort = "sets",
obsCatch = "Catch",
catchUnit = "number",
catchType = "dead discard",
logNum = NA,
sampleUnit = "trips",
factorVariables = c("Year","season"),
numericVariables = NA,
EstimateBycatch = TRUE,
baseDir = getwd(),
runName = "SimulatedExample",
runDescription = "Example with simulated data",
common = "Simulated species",
sp = "Genus species",
reportType = "html"
)} # }